# By using this file you agree to the legally binding terms of use found at # https://github.com/google-deepmind/alphafold3/blob/main/OUTPUT_TERMS_OF_USE.md. # To request access to the AlphaFold 3 model parameters, follow the process set # out at https://github.com/google-deepmind/alphafold3. You may only use these if # received directly from Google. Use is subject to terms of use available at # https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md. data_spkb14541 # _entry.id spkb14541 # loop_ _atom_type.symbol C N O S # loop_ _audit_author.name _audit_author.pdbx_ordinal "Google DeepMind" 1 "Isomorphic Labs" 2 # _audit_conform.dict_location https://raw.githubusercontent.com/ihmwg/ModelCIF/master/dist/mmcif_ma.dic _audit_conform.dict_name mmcif_ma.dic _audit_conform.dict_version 1.4.5 # loop_ _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_smiles _chem_comp.pdbx_synonyms _chem_comp.type "C3 H7 N O2" 89.093 ALA y ALANINE C[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C6 H15 N4 O2" 175.209 ARG y ARGININE C(C[C@@H](C(=O)O)N)CNC(=[NH2+])N ? "L-PEPTIDE LINKING" "C6 H13 N O2" 131.173 LEU y LEUCINE CC(C)C[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C5 H11 N O2 S" 149.211 MET y METHIONINE CSCC[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C5 H9 N O2" 115.130 PRO y PROLINE C1C[C@H](NC1)C(=O)O ? "L-PEPTIDE LINKING" "C3 H7 N O3" 105.093 SER y SERINE C([C@@H](C(=O)O)N)O ? "L-PEPTIDE LINKING" "C4 H9 N O3" 119.119 THR y THREONINE C[C@H]([C@@H](C(=O)O)N)O ? "L-PEPTIDE LINKING" # _citation.book_publisher ? _citation.country UK _citation.id primary _citation.journal_full Nature _citation.journal_id_ASTM NATUAS _citation.journal_id_CSD 0006 _citation.journal_id_ISSN 0028-0836 _citation.journal_volume 630 _citation.page_first 493 _citation.page_last 500 _citation.pdbx_database_id_DOI 10.1038/s41586-024-07487-w _citation.pdbx_database_id_PubMed 38718835 _citation.title "Accurate structure prediction of biomolecular interactions with AlphaFold 3" _citation.year 2024 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary "Google DeepMind" 1 primary "Isomorphic Labs" 2 # _entity.id 1 _entity.pdbx_description . _entity.type polymer # _entity_poly.entity_id 1 _entity_poly.pdbx_strand_id A _entity_poly.type polypeptide(L) # loop_ _entity_poly_seq.entity_id _entity_poly_seq.hetero _entity_poly_seq.mon_id _entity_poly_seq.num 1 n MET 1 1 n ALA 2 1 n PRO 3 1 n PRO 4 1 n ALA 5 1 n ALA 6 1 n ARG 7 1 n LEU 8 1 n ALA 9 1 n LEU 10 1 n LEU 11 1 n SER 12 1 n ALA 13 1 n ALA 14 1 n ALA 15 1 n LEU 16 1 n THR 17 1 n LEU 18 1 n ALA 19 # _ma_data.content_type "model coordinates" _ma_data.id 1 _ma_data.name Model # _ma_model_list.data_id 1 _ma_model_list.model_group_id 1 _ma_model_list.model_group_name "AlphaFold-beta-20231127 (3.0.0 @ 2025-07-03 04:21:20)" _ma_model_list.model_id 1 _ma_model_list.model_name "Top ranked model" _ma_model_list.model_type "Ab initio model" _ma_model_list.ordinal_id 1 # loop_ _ma_protocol_step.method_type _ma_protocol_step.ordinal_id _ma_protocol_step.protocol_id _ma_protocol_step.step_id "coevolution MSA" 1 1 1 "template search" 2 1 2 modeling 3 1 3 # loop_ _ma_qa_metric.id _ma_qa_metric.mode _ma_qa_metric.name _ma_qa_metric.software_group_id _ma_qa_metric.type 1 global pLDDT 1 pLDDT 2 local pLDDT 1 pLDDT # _ma_qa_metric_global.metric_id 1 _ma_qa_metric_global.metric_value 95.87 _ma_qa_metric_global.model_id 1 _ma_qa_metric_global.ordinal_id 1 # loop_ _ma_qa_metric_local.label_asym_id _ma_qa_metric_local.label_comp_id _ma_qa_metric_local.label_seq_id _ma_qa_metric_local.metric_id _ma_qa_metric_local.metric_value _ma_qa_metric_local.model_id _ma_qa_metric_local.ordinal_id A MET 1 2 85.35 1 1 A ALA 2 2 93.22 1 2 A PRO 3 2 95.50 1 3 A PRO 4 2 96.26 1 4 A ALA 5 2 97.69 1 5 A ALA 6 2 98.29 1 6 A ARG 7 2 93.72 1 7 A LEU 8 2 96.96 1 8 A ALA 9 2 98.40 1 9 A LEU 10 2 97.06 1 10 A LEU 11 2 97.25 1 11 A SER 12 2 97.34 1 12 A ALA 13 2 98.49 1 13 A ALA 14 2 98.42 1 14 A ALA 15 2 98.57 1 15 A LEU 16 2 97.52 1 16 A THR 17 2 96.66 1 17 A LEU 18 2 96.47 1 18 A ALA 19 2 93.60 1 19 # _ma_software_group.group_id 1 _ma_software_group.ordinal_id 1 _ma_software_group.software_id 1 # _ma_target_entity.data_id 1 _ma_target_entity.entity_id 1 _ma_target_entity.origin . # _ma_target_entity_instance.asym_id A _ma_target_entity_instance.details . _ma_target_entity_instance.entity_id 1 # loop_ _pdbx_data_usage.details _pdbx_data_usage.id _pdbx_data_usage.type _pdbx_data_usage.url ;Non-commercial use only, by using this file you agree to the terms of use found at https://github.com/google-deepmind/alphafold3/blob/main/OUTPUT_TERMS_OF_USE.md. To request access to the AlphaFold 3 model parameters, follow the process set out at https://github.com/google-deepmind/alphafold3. You may only use these if received directly from Google. Use is subject to terms of use available at https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md. ; 1 license https://github.com/google-deepmind/alphafold3/blob/main/OUTPUT_TERMS_OF_USE.md ;AlphaFold 3 and its output are not intended for, have not been validated for, and are not approved for clinical use. They are provided "as-is" without any warranty of any kind, whether expressed or implied. No warranty is given that use shall not infringe the rights of any third party. ; 2 disclaimer ? # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.hetero _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.seq_id A 1 1 n MET . 1 A 1 A 2 1 n ALA . 2 A 2 A 3 1 n PRO . 3 A 3 A 4 1 n PRO . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n ARG . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n SER . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n LEU . 16 A 16 A 17 1 n THR . 17 A 17 A 18 1 n LEU . 18 A 18 A 19 1 n ALA . 19 A 19 # _software.classification other _software.date ? _software.description "Structure prediction" _software.name AlphaFold _software.pdbx_ordinal 1 _software.type package _software.version "AlphaFold-beta-20231127 (9ceee3b5f7825b611ab42eaad843248507ced2da1e745fa3b3d93c6c4ad3ca74)" # _struct_asym.entity_id 1 _struct_asym.id A # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num ATOM 1 N N . MET A 1 1 ? -13.871 -4.500 -7.348 1.00 90.68 1 A 1 ATOM 2 C CA . MET A 1 1 ? -12.831 -3.671 -6.716 1.00 90.33 1 A 1 ATOM 3 C C . MET A 1 1 ? -12.382 -4.302 -5.405 1.00 91.61 1 A 1 ATOM 4 O O . MET A 1 1 ? -13.176 -4.934 -4.713 1.00 89.69 1 A 1 ATOM 5 C CB . MET A 1 1 ? -13.356 -2.251 -6.463 1.00 87.18 1 A 1 ATOM 6 C CG . MET A 1 1 ? -12.278 -1.301 -5.979 1.00 81.20 1 A 1 ATOM 7 S SD . MET A 1 1 ? -12.843 0.413 -5.925 1.00 80.23 1 A 1 ATOM 8 C CE . MET A 1 1 ? -13.946 0.341 -4.519 1.00 71.92 1 A 1 ATOM 9 N N . ALA A 1 2 ? -11.113 -4.126 -5.043 1.00 89.73 2 A 1 ATOM 10 C CA . ALA A 1 2 ? -10.571 -4.688 -3.807 1.00 93.76 2 A 1 ATOM 11 C C . ALA A 1 2 ? -11.193 -4.015 -2.582 1.00 95.87 2 A 1 ATOM 12 O O . ALA A 1 2 ? -11.614 -2.859 -2.654 1.00 95.11 2 A 1 ATOM 13 C CB . ALA A 1 2 ? -9.056 -4.513 -3.781 1.00 91.61 2 A 1 ATOM 14 N N . PRO A 1 3 ? -11.237 -4.727 -1.431 1.00 95.92 3 A 1 ATOM 15 C CA . PRO A 1 3 ? -11.802 -4.169 -0.202 1.00 96.82 3 A 1 ATOM 16 C C . PRO A 1 3 ? -10.985 -2.972 0.287 1.00 97.77 3 A 1 ATOM 17 O O . PRO A 1 3 ? -9.782 -2.884 0.007 1.00 97.35 3 A 1 ATOM 18 C CB . PRO A 1 3 ? -11.744 -5.338 0.798 1.00 95.18 3 A 1 ATOM 19 C CG . PRO A 1 3 ? -10.722 -6.275 0.238 1.00 91.89 3 A 1 ATOM 20 C CD . PRO A 1 3 ? -10.791 -6.103 -1.258 1.00 93.57 3 A 1 ATOM 21 N N . PRO A 1 4 ? -11.618 -2.031 1.042 1.00 96.79 4 A 1 ATOM 22 C CA . PRO A 1 4 ? -10.926 -0.828 1.530 1.00 97.12 4 A 1 ATOM 23 C C . PRO A 1 4 ? -9.720 -1.150 2.405 1.00 97.90 4 A 1 ATOM 24 O O . PRO A 1 4 ? -8.702 -0.453 2.343 1.00 97.59 4 A 1 ATOM 25 C CB . PRO A 1 4 ? -12.009 -0.071 2.316 1.00 95.84 4 A 1 ATOM 26 C CG . PRO A 1 4 ? -13.047 -1.102 2.624 1.00 93.32 4 A 1 ATOM 27 C CD . PRO A 1 4 ? -13.002 -2.079 1.481 1.00 95.26 4 A 1 ATOM 28 N N . ALA A 1 5 ? -9.813 -2.202 3.229 1.00 97.18 5 A 1 ATOM 29 C CA . ALA A 1 5 ? -8.705 -2.598 4.096 1.00 97.85 5 A 1 ATOM 30 C C . ALA A 1 5 ? -7.487 -3.016 3.274 1.00 98.32 5 A 1 ATOM 31 O O . ALA A 1 5 ? -6.352 -2.667 3.601 1.00 98.01 5 A 1 ATOM 32 C CB . ALA A 1 5 ? -9.145 -3.741 5.009 1.00 97.10 5 A 1 ATOM 33 N N . ALA A 1 6 ? -7.721 -3.761 2.201 1.00 98.16 6 A 1 ATOM 34 C CA . ALA A 1 6 ? -6.641 -4.201 1.322 1.00 98.36 6 A 1 ATOM 35 C C . ALA A 1 6 ? -6.006 -3.010 0.608 1.00 98.56 6 A 1 ATOM 36 O O . ALA A 1 6 ? -4.787 -2.964 0.423 1.00 98.30 6 A 1 ATOM 37 C CB . ALA A 1 6 ? -7.171 -5.208 0.305 1.00 98.09 6 A 1 ATOM 38 N N . ARG A 1 7 ? -6.832 -2.024 0.217 1.00 98.13 7 A 1 ATOM 39 C CA . ARG A 1 7 ? -6.343 -0.818 -0.456 1.00 98.32 7 A 1 ATOM 40 C C . ARG A 1 7 ? -5.418 -0.030 0.463 1.00 98.46 7 A 1 ATOM 41 O O . ARG A 1 7 ? -4.346 0.403 0.045 1.00 98.27 7 A 1 ATOM 42 C CB . ARG A 1 7 ? -7.532 0.042 -0.891 1.00 98.05 7 A 1 ATOM 43 C CG . ARG A 1 7 ? -7.123 1.311 -1.630 1.00 95.09 7 A 1 ATOM 44 C CD . ARG A 1 7 ? -6.476 0.995 -2.966 1.00 93.71 7 A 1 ATOM 45 N NE . ARG A 1 7 ? -6.153 2.215 -3.702 1.00 91.49 7 A 1 ATOM 46 C CZ . ARG A 1 7 ? -5.611 2.241 -4.910 1.00 90.04 7 A 1 ATOM 47 N NH1 . ARG A 1 7 ? -5.321 1.119 -5.539 1.00 84.29 7 A 1 ATOM 48 N NH2 . ARG A 1 7 ? -5.351 3.402 -5.489 1.00 85.11 7 A 1 ATOM 49 N N . LEU A 1 8 ? -5.813 0.157 1.717 1.00 98.31 8 A 1 ATOM 50 C CA . LEU A 1 8 ? -4.997 0.880 2.691 1.00 98.26 8 A 1 ATOM 51 C C . LEU A 1 8 ? -3.692 0.140 2.962 1.00 98.37 8 A 1 ATOM 52 O O . LEU A 1 8 ? -2.631 0.757 3.066 1.00 98.14 8 A 1 ATOM 53 C CB . LEU A 1 8 ? -5.772 1.059 3.997 1.00 98.05 8 A 1 ATOM 54 C CG . LEU A 1 8 ? -6.906 2.075 3.902 1.00 96.01 8 A 1 ATOM 55 C CD1 . LEU A 1 8 ? -7.764 2.017 5.154 1.00 94.34 8 A 1 ATOM 56 C CD2 . LEU A 1 8 ? -6.342 3.482 3.728 1.00 94.23 8 A 1 ATOM 57 N N . ALA A 1 9 ? -3.758 -1.182 3.078 1.00 98.46 9 A 1 ATOM 58 C CA . ALA A 1 9 ? -2.570 -1.998 3.317 1.00 98.43 9 A 1 ATOM 59 C C . ALA A 1 9 ? -1.583 -1.875 2.157 1.00 98.59 9 A 1 ATOM 60 O O . ALA A 1 9 ? -0.374 -1.778 2.369 1.00 98.33 9 A 1 ATOM 61 C CB . ALA A 1 9 ? -2.972 -3.457 3.518 1.00 98.19 9 A 1 ATOM 62 N N . LEU A 1 10 ? -2.101 -1.858 0.936 1.00 98.18 10 A 1 ATOM 63 C CA . LEU A 1 10 ? -1.261 -1.728 -0.252 1.00 98.14 10 A 1 ATOM 64 C C . LEU A 1 10 ? -0.557 -0.374 -0.282 1.00 98.26 10 A 1 ATOM 65 O O . LEU A 1 10 ? 0.642 -0.293 -0.558 1.00 98.06 10 A 1 ATOM 66 C CB . LEU A 1 10 ? -2.113 -1.908 -1.511 1.00 98.05 10 A 1 ATOM 67 C CG . LEU A 1 10 ? -1.311 -1.887 -2.814 1.00 96.18 10 A 1 ATOM 68 C CD1 . LEU A 1 10 ? -0.379 -3.093 -2.897 1.00 94.84 10 A 1 ATOM 69 C CD2 . LEU A 1 10 ? -2.250 -1.883 -4.010 1.00 94.77 10 A 1 ATOM 70 N N . LEU A 1 11 ? -1.293 0.694 0.006 1.00 98.14 11 A 1 ATOM 71 C CA . LEU A 1 11 ? -0.723 2.041 0.023 1.00 98.03 11 A 1 ATOM 72 C C . LEU A 1 11 ? 0.327 2.176 1.120 1.00 98.17 11 A 1 ATOM 73 O O . LEU A 1 11 ? 1.387 2.765 0.909 1.00 98.04 11 A 1 ATOM 74 C CB . LEU A 1 11 ? -1.835 3.074 0.233 1.00 97.98 11 A 1 ATOM 75 C CG . LEU A 1 11 ? -2.767 3.225 -0.968 1.00 96.86 11 A 1 ATOM 76 C CD1 . LEU A 1 11 ? -3.980 4.061 -0.588 1.00 95.42 11 A 1 ATOM 77 C CD2 . LEU A 1 11 ? -2.037 3.877 -2.137 1.00 95.39 11 A 1 ATOM 78 N N . SER A 1 12 ? 0.046 1.619 2.291 1.00 98.33 12 A 1 ATOM 79 C CA . SER A 1 12 ? 0.977 1.666 3.414 1.00 98.26 12 A 1 ATOM 80 C C . SER A 1 12 ? 2.254 0.897 3.095 1.00 98.49 12 A 1 ATOM 81 O O . SER A 1 12 ? 3.357 1.369 3.370 1.00 98.37 12 A 1 ATOM 82 C CB . SER A 1 12 ? 0.325 1.086 4.668 1.00 97.71 12 A 1 ATOM 83 O OG . SER A 1 12 ? 1.214 1.171 5.755 1.00 92.91 12 A 1 ATOM 84 N N . ALA A 1 13 ? 2.112 -0.280 2.497 1.00 98.55 13 A 1 ATOM 85 C CA . ALA A 1 13 ? 3.262 -1.100 2.135 1.00 98.53 13 A 1 ATOM 86 C C . ALA A 1 13 ? 4.143 -0.385 1.113 1.00 98.69 13 A 1 ATOM 87 O O . ALA A 1 13 ? 5.370 -0.402 1.221 1.00 98.46 13 A 1 ATOM 88 C CB . ALA A 1 13 ? 2.790 -2.442 1.579 1.00 98.24 13 A 1 ATOM 89 N N . ALA A 1 14 ? 3.524 0.258 0.129 1.00 98.52 14 A 1 ATOM 90 C CA . ALA A 1 14 ? 4.267 0.992 -0.890 1.00 98.44 14 A 1 ATOM 91 C C . ALA A 1 14 ? 5.024 2.164 -0.273 1.00 98.62 14 A 1 ATOM 92 O O . ALA A 1 14 ? 6.186 2.408 -0.610 1.00 98.38 14 A 1 ATOM 93 C CB . ALA A 1 14 ? 3.310 1.490 -1.971 1.00 98.15 14 A 1 ATOM 94 N N . ALA A 1 15 ? 4.387 2.889 0.644 1.00 98.66 15 A 1 ATOM 95 C CA . ALA A 1 15 ? 5.010 4.029 1.309 1.00 98.64 15 A 1 ATOM 96 C C . ALA A 1 15 ? 6.205 3.589 2.154 1.00 98.71 15 A 1 ATOM 97 O O . ALA A 1 15 ? 7.260 4.219 2.125 1.00 98.39 15 A 1 ATOM 98 C CB . ALA A 1 15 ? 3.985 4.747 2.178 1.00 98.44 15 A 1 ATOM 99 N N . LEU A 1 16 ? 6.052 2.503 2.902 1.00 98.67 16 A 1 ATOM 100 C CA . LEU A 1 16 ? 7.127 1.990 3.749 1.00 98.60 16 A 1 ATOM 101 C C . LEU A 1 16 ? 8.295 1.479 2.908 1.00 98.66 16 A 1 ATOM 102 O O . LEU A 1 16 ? 9.454 1.633 3.286 1.00 98.22 16 A 1 ATOM 103 C CB . LEU A 1 16 ? 6.597 0.868 4.644 1.00 98.37 16 A 1 ATOM 104 C CG . LEU A 1 16 ? 5.656 1.349 5.750 1.00 97.19 16 A 1 ATOM 105 C CD1 . LEU A 1 16 ? 4.988 0.159 6.419 1.00 95.45 16 A 1 ATOM 106 C CD2 . LEU A 1 16 ? 6.418 2.166 6.786 1.00 94.99 16 A 1 ATOM 107 N N . THR A 1 17 ? 7.996 0.878 1.776 1.00 98.23 17 A 1 ATOM 108 C CA . THR A 1 17 ? 9.036 0.347 0.894 1.00 97.97 17 A 1 ATOM 109 C C . THR A 1 17 ? 9.879 1.470 0.291 1.00 98.12 17 A 1 ATOM 110 O O . THR A 1 17 ? 11.107 1.355 0.204 1.00 97.28 17 A 1 ATOM 111 C CB . THR A 1 17 ? 8.407 -0.486 -0.230 1.00 97.27 17 A 1 ATOM 112 O OG1 . THR A 1 17 ? 7.680 -1.575 0.331 1.00 94.35 17 A 1 ATOM 113 C CG2 . THR A 1 17 ? 9.478 -1.047 -1.153 1.00 93.37 17 A 1 ATOM 114 N N . LEU A 1 18 ? 9.228 2.558 -0.128 1.00 97.92 18 A 1 ATOM 115 C CA . LEU A 1 18 ? 9.923 3.682 -0.756 1.00 97.82 18 A 1 ATOM 116 C C . LEU A 1 18 ? 10.529 4.645 0.262 1.00 97.87 18 A 1 ATOM 117 O O . LEU A 1 18 ? 11.557 5.268 -0.008 1.00 97.02 18 A 1 ATOM 118 C CB . LEU A 1 18 ? 8.956 4.432 -1.676 1.00 97.35 18 A 1 ATOM 119 C CG . LEU A 1 18 ? 8.483 3.616 -2.883 1.00 96.24 18 A 1 ATOM 120 C CD1 . LEU A 1 18 ? 7.382 4.363 -3.622 1.00 94.25 18 A 1 ATOM 121 C CD2 . LEU A 1 18 ? 9.647 3.339 -3.828 1.00 93.30 18 A 1 ATOM 122 N N . ALA A 1 19 ? 9.888 4.786 1.430 1.00 96.87 19 A 1 ATOM 123 C CA . ALA A 1 19 ? 10.342 5.713 2.460 1.00 95.80 19 A 1 ATOM 124 C C . ALA A 1 19 ? 11.679 5.284 3.059 1.00 94.89 19 A 1 ATOM 125 O O . ALA A 1 19 ? 11.957 4.074 3.141 1.00 92.94 19 A 1 ATOM 126 C CB . ALA A 1 19 ? 9.285 5.853 3.549 1.00 93.65 19 A 1 ATOM 127 O OXT . ALA A 1 19 ? 12.463 6.161 3.464 1.00 87.43 19 A 1 #